[gmx-users] Re: gmx-users Digest, Vol 86, Issue 138
marco miele
marco.miele75 at gmail.com
Wed Jun 22 18:18:50 CEST 2011
2011/6/22 <gmx-users-request at gromacs.org>
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> Today's Topics:
>
> 1. Re: PMF and appending simulation: -pf and -px flags (gromacs
> 4.0.7) (Justin A. Lemkul)
> 2. Re: DPPC temperatur setting (Justin A. Lemkul)
> 3. in preparation for 4.5.5 and 4.6 releases (Rossen Apostolov)
> 4. plateau in msd (glass transition); ref_t (Anja Kuhnhold)
> 5. Re: Programs to add residues (Michael Lerner)
> 6. Re: Autocorrelation of dipole moment (Andr? Farias de Moura)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 22 Jun 2011 06:14:06 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] PMF and appending simulation: -pf and -px
> flags (gromacs 4.0.7)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E01C06E.9080800 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Shay Teaching wrote:
> > Hi everyone,
> >
> > Does the appending option also work when doing PMF?
> > I have a simulation that crashed in the middle (not-gromacs-related),
> > and now I want to continue from where it stopped.
> > But using the -append option does not seem to continue writing to the
> > files specified in -px and -pf.
> >
>
> Appending can be done, but without seeing your actual series of commands,
> no one
> can offer you any useful advice or insight as to why it isn't working in
> your case.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 22 Jun 2011 06:16:52 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] DPPC temperatur setting
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E01C114.20709 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> marco miele wrote:
> > Hi everybody
> > I am starting to analyze the membrane system composed with DPPC lipids,
> > I saw both MD membrane paper and KALP-15 tutorial to setting a 323K.
> > My question is That
> > in this way we working around 50 C, which is not body temperature 37 C,
> > this is not realistic approach,
> > If my interest is to obtain data that respects the human body condition
> > can I to setting the temperature at 310 = 37 C or a make mistake and
> > obtain artefacts data.
> >
>
> The reason for using 323 K in the case of DPPC is that (1) it is a common
> experimental temperature and (2) it is above the phase-transition
> temperature
> for this lipid. Anywhere below 315 K or so and your membrane will enter a
> gel
> phase, which is not representative of the membrane properties in vivo.
> Working
> with DPPC thus involves a tradeoff - you can either produce a liquid phase
> (like
> in vivo) or physiological temperature (while losing the physical properties
> associated with cellular membranes). The latter is often disfavored, but
> the
> end result is that DPPC is simply a poor choice to represent cell
> membranes, but
> is often a useful in vitro model, depending on your aims and available
> data.
>
> -Justin
>
>
>
My aim is to obtain a good model for analyzing a receptor protein (not
channel).
I prepared a system with DPPC CHOL and Protein, but I am not sure fore only
temperature.
"The latter is often disfavored, but the end result is that DPPC is simply a
poor choice to represent cell membranes,
but is often a useful in vitro model, depending on your aims and available
data."
What kind of lipid you suggest me, in vision of system indicated before DPPC
CHOL PROTEIN.
I am interesting to understand if the conformation of protein is mantained
in diff % of CHOL.
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 22 Jun 2011 13:10:12 +0200
> From: Rossen Apostolov <rossen at kth.se>
> Subject: [gmx-users] in preparation for 4.5.5 and 4.6 releases
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>,
> Discussion list for GROMACS development <gmx-developers at gromacs.org
> >,
> gmx-announce at gromacs.org
> Message-ID: <4E01CD94.8050205 at kth.se>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> We are preparing for a new maintenance release 4.5.5. It will fix
> critical open issues with previous releases, so please file your reports
> in redmine.gromacs.org by the end of June.
>
> After the 4.5.5 release, the stable branch will be frozen for bugfixes
> only, and new functionality will be added to a new release-4-6-patches
> branch, a fork of release-4-5-patches right after 4.5.5.
>
> Currently the plan is to have in 4.6:
>
> * faster native GPU implementation supporting most of current
> Gromacs features
> * collective I/O
> * lambda dynamics and other free energy extensions
> * AdResS (http://www.mpip-mainz.mpg.de/~poma/multiscale/adress.php)
> * advanced rotational pulling
> * file history
> * several new tools
> * autoconf removed - support for building only with CMake
>
> Code from contributors will be considered for inclusion also but it's
> necessary that
>
> * comes with support for the code in future releases, e.g. port it
> to the completely new C++ structure in the 5.0 release and
> maintain it after
> * builds against 4.5.5
> * produces scientifically reliable results
> * works in parallel and doesn't affect the performance
> * comes with regression test sets for the new features
> * has the necessary documentation for usage
>
> After 4.5.5 bug fixes need to be applied as:
>
> * bugs in 4.5.5:
> o fix in 4.5.5 -> fix in 4.6 -> fix in master
> * bugs in the new features introduced in 4.6:
> o fix in 4.6 -> fix in master
>
>
> The plan is to have 4.5.5 around end of July, and 4.6-gamma a month later.
>
> Rossen
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> ------------------------------
>
> Message: 4
> Date: Wed, 22 Jun 2011 13:34:58 +0200
> From: Anja Kuhnhold <anja.kuhnhold at physik.uni-halle.de>
> Subject: [gmx-users] plateau in msd (glass transition); ref_t
> To: gmx-users at gromacs.org
> Message-ID: <fac78671a57f.4e01ef82 at uni-halle.de>
> Content-Type: text/plain; charset=us-ascii
>
> Hi everyone,
>
> I'm simulating a bead-spring polymer model (1600 chains and 10 beads per
> chain in a 26.6^3 box with pbc) with LJ and FENE potentials.
> I calculate the mean-square-displacement for different temperatures. For
> T=0.46 (in LJ units) I expected to get a plateau in the msd curve (glass
> transition)- but there is none. The curve for T=0.46 is similar to the one
> for T=1.0 (above glass transition) with only a small shift to lower values-
> but no plateau.
>
> My .mdp-files look as follows:
>
> integrator = md-vv
> dt = 0.0035
> nsteps = 100
> nstxout = 1
> nstvout = 1
> nstfout = 1
> nstlog = 1
> ns_type = grid
> pbc = xyz
> periodic_molecules = yes
> rvdw = 1.12
> rlist = 1.3
> tcoupl = nose-hoover
> tc-grps = System
> tau_t = 20
> ref_t = 55.32
> vdwtype = Shift
> rcoulomb = 1.12
> coulombtype = Reaction-Field-zero
> epsilon_rf = 0
>
> I have 6 of these files, where only nsteps and nst*out are changed by
> multiplying them by 10 (so I get overlapping intervals for the msd).
>
>
> Is the ref_t correct? The results in the md.log file say T is about 89.
> Why do I not get a plateau? What did I not consider?
>
> Thanks in advance.
> Anja
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 22 Jun 2011 08:52:32 -0400
> From: Michael Lerner <mglerner at gmail.com>
> Subject: Re: [gmx-users] Programs to add residues
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTim7dbY4uwefcc38HiPJw8TZ7jZeVA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Tue, Jun 21, 2011 at 4:12 PM, Chris Neale <chris.neale at utoronto.ca
> >wrote:
>
> > Try "Loopy". You can get it to build termini in addition to loops.
> >
> >
> http://wiki.c2b2.columbia.edu/**honiglab_public/index.php/**Software:Loopy
> <http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy>
> >
> >
> I've also seen people use PyMOL's builder to do this. Either way, you'll
> need to take (a lot of) extra care to minimize your linker and make sure
> that it looks reasonable.
>
> -Michael
>
>
> > Nevertheless, I'd suggest simply omitting that part of the protein and
> > capping your new terminus to remove the charge. You will have more
> > difficulties converging the conformation of the unstructured terminus
> than
> > you may expect.
>
>
> > CHris.
> >
> > -- original message --
> >
> > Hi all,
> >
> > Is there a program that allows the user to add residues to the N and C
> > terminus, without using the electron density? I would like to add a
> > short linker to my protein which doesn't exist in the electron
> > density.
> >
> > Thanks a lot,
> >
> > Sincerely,
> > Zack
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
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>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
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> ------------------------------
>
> Message: 6
> Date: Wed, 22 Jun 2011 10:53:21 -0300
> From: Andr? Farias de Moura <moura at ufscar.br>
> Subject: Re: [gmx-users] Autocorrelation of dipole moment
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTi=zdVSNcy9n7n=AVmTdHqohEd3mXQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> sure, the ACF for a vector gives you the average cosine between that vector
> at time t=0 and the same vector at a later time lag, thus negative values
> may
> be seen as an inversion of the direction to which the vector points
> out (-1 would
> be the value for a vector lying 180 degrees away from the direction at
> t=0).
>
> best
>
> Andre
>
> On Tue, Jun 21, 2011 at 8:29 PM, Chathurika Abeyrathne
> <c.abeyrathne at student.unimelb.edu.au> wrote:
> >
> >
> > Hi,
> >
> > Is it possible to get negative values for normalized autocorrelation of
> > total dipole moment.
> >
> > Thank you.
> >
> >
> > Regards,
> > Chathurika.
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
> ------------------------------
>
> --
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> End of gmx-users Digest, Vol 86, Issue 138
> ******************************************
>
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